% This file was created with JabRef 2.3.1.
% Encoding: UTF-8

@INBOOK{reg-motifs-molbilcell,
  chapter = {DNA-binding Motifs in Gene Regulatory Proteins},
  title = {Molecular Biology of the Cell},
  publisher = {Garland Science},
  year = {2008},
  editor = {Bruce Alberts},
  author = {Bruce Alberts},
  owner = {krab},
  timestamp = {2010.06.01}
}

@ARTICLE{araki1998allosteric,
  author = {Araki, M. and Okuno, Y. and Hara, Y. and Sugiura, Y.},
  title = {{Allosteric regulation of a ribozyme activity through ligand-induced
	conformational change}},
  journal = {Nucleic acids research},
  year = {1998},
  volume = {26},
  pages = {3379},
  number = {14},
  publisher = {Oxford Univ Press}
}

@ARTICLE{PrasadBahadur2004943SpecNonspec,
  author = {Ranjit Prasad Bahadur and Pinak Chakrabarti and Francis Rodier and
	Joël Janin},
  title = {A Dissection of Specific and Non-specific Protein-Protein Interfaces},
  journal = {Journal of Molecular Biology},
  year = {2004},
  volume = {336},
  pages = {943 - 955},
  number = {4},
  doi = {DOI: 10.1016/j.jmb.2003.12.073},
  issn = {0022-2836},
  keywords = {protein-protein interaction},
  url = {http://www.sciencedirect.com/science/article/B6WK7-4BRTKR9-C/2/ce716dee1132d2605f8e1c96d1154253}
}

@ARTICLE{geom-criteria,
  author = {Baker, EN and Hubbard, RE},
  title = {{Hydrogen bonding in globular proteins}},
  journal = {Progress in biophysics and molecular biology},
  year = {1984},
  volume = {44},
  pages = {97--179},
  number = {2},
  publisher = {Elsevier}
}

@ARTICLE{pdb-ref,
  author = {Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N.,
	Weissig, H. et al.},
  title = {The Protein Data Bank},
  journal = {Nucleic acids research},
  year = {2000},
  volume = {28},
  pages = {235-242},
  owner = {krab},
  timestamp = {2010.06.01}
}

@MISC{biopython-install,
  author = {Brad Chapman and others},
  title = {Biopython Installation},
  howpublished = {\url{http://www.biopython.org/DIST/docs/install/Installation.html}
	(1.\,6.\,2010)},
  owner = {krab},
  timestamp = {2010.06.03}
}

@ARTICLE{biopython,
  author = {Cock, P.J.A. and Antao, T. and Chang, J.T. and Chapman, B.A. and
	Cox, C.J. and Dalke, A. and Friedberg, I. and Hamelryck, T. and Kauff,
	F. and Wilczynski, B. and others},
  title = {{Biopython: freely available Python tools for computational molecular
	biology and bioinformatics}},
  journal = {Bioinformatics},
  year = {2009},
  volume = {25},
  pages = {1422},
  number = {11},
  publisher = {Oxford Univ Press}
}

@ARTICLE{Coulocheri20071291,
  author = {Stavroula A. Coulocheri and Diomidis G. Pigis and Kostas A. Papavassiliou
	and Athanasios G. Papavassiliou},
  title = {Hydrogen bonds in protein-DNA complexes: Where geometry meets plasticity},
  journal = {Biochimie},
  year = {2007},
  volume = {89},
  pages = {1291 - 1303},
  number = {11},
  doi = {DOI: 10.1016/j.biochi.2007.07.020},
  issn = {0300-9084},
  keywords = {Hydrogen bond (H-bond)},
  url = {http://www.sciencedirect.com/science/article/B6VRJ-4P9SNJ2-7/2/e8fbe900626db6adcdf6994f6881afdb}
}

@ARTICLE{Dickerson1998DNAbending,
  author = {Dickerson, RE},
  title = {{DNA bending: the prevalence of kinkiness and the virtues of normality}},
  journal = {Nucl. Acids Res.},
  year = {1998},
  volume = {26},
  pages = {1906-1926},
  number = {8},
  doi = {10.1093/nar/26.8.1906},
  eprint = {http://nar.oxfordjournals.org/cgi/reprint/26/8/1906.pdf},
  url = {http://nar.oxfordjournals.org/cgi/content/abstract/26/8/1906}
}

@ARTICLE{ellis2001macromolecular,
  author = {Ellis, R.J.},
  title = {{Macromolecular crowding: an important but neglected aspect of the
	intracellular environment}},
  journal = {Current opinion in structural biology},
  year = {2001},
  volume = {11},
  pages = {114--119},
  number = {1},
  publisher = {Elsevier}
}

@ARTICLE{Fuller1959,
  author = {Fuller, W.},
  title = {Hydrogen Bond Lengths and Angles Observed in Crystals},
  journal = {The Journal of Physical Chemistry},
  year = {1959},
  volume = {63},
  pages = {1705--1717},
  number = {10},
  month = oct,
  comment = {doi: 10.1021/j150580a035},
  issn = {0022-3654},
  owner = {krab},
  publisher = {American Chemical Society},
  timestamp = {2010.06.02},
  url = {http://dx.doi.org/10.1021/j150580a035}
}

@ARTICLE{henrick2008remediation,
  author = {Henrick, K. and Feng, Z. and Bluhm, W.F. and Dimitropoulos, D. and
	Doreleijers, J.F. and Dutta, S. and Flippen-Anderson, J.L. and Ionides,
	J. and Kamada, C. and Krissinel, E. and others},
  title = {{Remediation of the protein data bank archive}},
  journal = {Nucleic acids research},
  year = {2008},
  volume = {36},
  pages = {D426},
  number = {Database issue},
  publisher = {Oxford Univ Press}
}

@TECHREPORT{naccess,
  author = {Hubbard, S. J. and Thornton, J. M.},
  title = {'NACCESS', computer program.},
  institution = {Department of Biochemistry Molecular Biology, University College
	London},
  year = {1993},
  howpublished = {\url{http://www.bioinf.manchester.ac.uk/naccess/}}
}

@INBOOK{binding-site,
  chapter = {4.2 Structural Biology of Binding Sites},
  pages = {101-102},
  title = {Chemogenomics in Drug Discovery},
  publisher = {Wiley-VCH},
  year = {2004},
  editor = {Hugo Kubinyi, Gerhard Müller},
  author = {Hugo Kubinyi, Gerhard Müller},
  owner = {krab},
  timestamp = {2010.06.01}
}

@ARTICLE{VMD96,
  author = {William Humphrey and Andrew Dalke and Klaus Schulten},
  title = {{VMD} -- {V}isual {M}olecular {D}ynamics},
  journal = {Journal of Molecular Graphics},
  year = {1996},
  volume = {14},
  pages = {33-38},
  tbreference = {222},
  tbstatus = {Published.}
}

@TECHREPORT{pdb-format,
  author = {J. Callaway, M. Cummings, B. Deroski and others},
  title = {Protein Data Bank Contents Guide: Atomic Coordinate Entry Format
	Description},
  institution = {wwPDB},
  year = {2008},
  month = {October},
  note = {Version 3.2},
  owner = {krab},
  timestamp = {2010.05.11},
  url = {http://www.wwpdb.org/documentation/format32/v3.2.html}
}

@ARTICLE{Jones1999,
  author = {Susan Jones and Paul van Heyningen and Helen M. Berman and Janet
	M. Thornton},
  title = {Protein-DNA interactions: a structural analysis},
  journal = {Journal of Molecular Biology},
  year = {1999},
  volume = {287},
  pages = {877 - 896},
  number = {5},
  doi = {DOI: 10.1006/jmbi.1999.2659},
  issn = {0022-2836},
  keywords = {Protein-DNA complex},
  url = {http://www.sciencedirect.com/science/article/B6WK7-45R881M-NW/2/d069b483e5711f0a730b47e430a45a75}
}

@PHDTHESIS{kahraman-thesis,
  author = {Abdullah Kahraman},
  title = {The Geometry and Physicochemistry of Protein Binding Sites and Ligands
	and their Detection in Electron Density Maps},
  school = {European Bioinformatics Institute, Clare College and Faculty of Biology,
	University of Cambridge},
  year = {2009},
  owner = {krab},
  timestamp = {2010.06.01}
}

@INBOOK{inhibice,
  chapter = {inhibice enzymů allosterická},
  title = {Biochemické pojmy : výkladový slovník [online]},
  publisher = {VŠCHT Praha},
  year = {2007},
  author = {Kodíček, M.},
  owner = {krab},
  timestamp = {2010.06.01}
}

@ARTICLE{luscombe2001amino,
  author = {Luscombe, N.M. and Laskowski, R.A. and Thornton, J.M.},
  title = {{Amino acid-base interactions: a three-dimensional analysis of protein-DNA
	interactions at an atomic level}},
  journal = {Nucleic Acids Research},
  year = {2001},
  volume = {29},
  pages = {2860-2874},
  number = {13},
  publisher = {Oxford Univ Press}
}

@ARTICLE{macheboeuf2005active,
  author = {Macheboeuf, P. and Di Guilmi, A.M. and Job, V. and Vernet, T. and
	Dideberg, O. and Dessen, A.},
  title = {{Active site restructuring regulates ligand recognition in class
	A penicillin-binding proteins}},
  journal = {Proceedings of the National Academy of Sciences of the United States
	of America},
  year = {2005},
  volume = {102},
  pages = {577},
  number = {3},
  publisher = {National Acad Sciences}
}

@ARTICLE{hbplus,
  author = {McDonald, I.K., Thornton, J.M.},
  title = {Satisfying hydrogen-bonding potential in proteins},
  journal = {J. Mol. Biol.},
  year = {1994},
  volume = {238},
  pages = {777-793},
  number = {5}
}

@ARTICLE{sqlite,
  author = {Owens, M.},
  title = {Embedding an {SQL} database with {SQL}ite},
  journal = {Linux Journal},
  year = {2003},
  volume = {110}
}

@ARTICLE{mmlib,
  author = {Painter, J. and Merritt, EA},
  title = {{mmLib Python toolkit for manipulating annotated structural models
	of biological macromolecules}},
  journal = {Journal of Applied Crystallography},
  year = {2004},
  volume = {37},
  pages = {174--178},
  number = {1},
  publisher = {International Union of Crystallography}
}

@BOOK{vdw-book,
  title = {Van der Waals forces: a handbook for biologists, chemists, engineers,
	and physicists},
  publisher = {Cambridge University Press},
  year = {2006},
  author = {Vozken Adrian Parsegian},
  owner = {krab},
  timestamp = {2010.06.02}
}

@INPROCEEDINGS{gcc-stack-protector,
  author = {Perry Wagle, Crispin Cowan},
  title = {StackGuard: Simple Stack Smash Protection for GCC},
  booktitle = {Proceedings of the GCC Developers Summit},
  year = {2003},
  pages = {243-255},
  month = {May},
  owner = {krab},
  timestamp = {2010.05.22}
}

@TECHREPORT{python-ref,
  author = {Guido van Rossum},
  title = {Python Reference Manual},
  institution = {CWI},
  year = {1995},
  month = {May},
  owner = {krab},
  timestamp = {2010.05.27}
}

@ARTICLE{python-integration,
  author = {Sanner, MF},
  title = {Python: A programming language for software integration and development},
  journal = {Journal of Molecular Graphics \& Modelling},
  year = {1999},
  volume = {17},
  pages = {57-61},
  number = {{1}},
  month = {{FEB}},
  address = {{655 AVENUE OF THE AMERICAS, NEW YORK, NY 10010 USA}},
  affiliation = {{Sanner, MF (Reprint Author), Scripps Res Inst, 10550 N Torrey Pines
	Rd, La Jolla, CA 92037 USA. Scripps Res Inst, La Jolla, CA 92037
	USA.}},
  doc-delivery-number = {{264CL}},
  issn = {{1093-3263}},
  journal-iso = {{J. Mol. Graph.}},
  language = {{English}},
  number-of-cited-references = {{2}},
  publisher = {{ELSEVIER SCIENCE INC}},
  subject-category = {{Biochemical Research Methods; Biochemistry \& Molecular Biology;
	Computer Science, Interdisciplinary Applications; Crystallography;
	Mathematical \& Computational Biology}},
  times-cited = {{168}},
  type = {{News Item}},
  unique-id = {{ISI:000084162500006}}
}

@MISC{dpc,
  author = {Sedlák, F.},
  title = {{dna-protein-contacts, Program pro sestavení databáze kontaktů a
	sada strukturních dat} [online]},
  howpublished = {\url{http://code.google.com/p/dna-protein-contacts/} (1.\,6.\,2010)},
  owner = {krab},
  timestamp = {2010.06.02}
}

@ARTICLE{svozil2008dna,
  author = {Svozil, D. and Kalina, J. and Omelka, M. and Schneider, B.},
  title = {{DNA conformations and their sequence preferences}},
  journal = {Nucleic Acids Research},
  year = {2008},
  volume = {36},
  pages = {3690-3706},
  number = {11},
  month = {May},
  doi = {10.1093/nar/gkn260},
  publisher = {Oxford Univ Press}
}

@ARTICLE{allosteric-inhibition-atp,
  author = {Tang, J. and Breaker, R. R.},
  title = {Mechanism for allosteric inhibition of an ATP-sensitive ribozyme},
  journal = {Nucl. Acids Res.},
  year = {1998},
  volume = {26},
  pages = {4214--4221},
  number = {18},
  month = {September},
  abstract = {10.1093/nar/26.18.4214},
  citeulike-article-id = {7231946},
  citeulike-linkout-0 = {http://dx.doi.org/10.1093/nar/26.18.4214},
  citeulike-linkout-1 = {http://nar.oxfordjournals.org/cgi/content/abstract/26/18/4214},
  citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/9722642},
  citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=9722642},
  day = {15},
  doi = {10.1093/nar/26.18.4214},
  posted-at = {2010-06-01 07:09:53},
  priority = {1},
  url = {http://dx.doi.org/10.1093/nar/26.18.4214}
}

@ARTICLE{von1994protein,
  author = {Von Hippel, PH},
  title = {{Protein-DNA recognition: new perspectives and underlying themes.}},
  journal = {Science (New York, NY)},
  year = {1994},
  volume = {263},
  pages = {769},
  number = {5148}
}

@BOOK{dna-protein-interactions-book,
  title = {DNA-Protein: Structural Interactions},
  publisher = {Oxford Univ Press},
  year = {1995},
  editor = {David M. J. Lilley},
  owner = {krab},
  timestamp = {2010.06.01}
}

@INBOOK{wm-contacts-inbook,
  chapter = {3.2 Water mediated contacts},
  pages = {23-24},
  title = {DNA-Protein: Structural Interactions},
  publisher = {Oxford Univ Press},
  year = {1995},
  editor = {David M. J. Lilley},
  owner = {krab},
  timestamp = {2010.06.01}
}

@MISC{hbplus-diff,
  title = {hbplus.diff},
  owner = {krab},
  timestamp = {2010.05.15}
}

@MISC{hbplus-web,
  title = {HBPLUS Home Page},
  howpublished = {\url{http://www.biochem.ucl.ac.uk/bsm/hbplus/} (1.\,6.\,2010)}
}

@MISC{hbplusl-manual,
  title = {HBPLUS v3.06 manual},
  howpublished = {\url{http://www.biochem.ucl.ac.uk/bsm/hbplus/hbplus.man} (1.\,6.\,2010)},
  note = {Distribuován s programem HBPLUS.},
  owner = {krab},
  timestamp = {2010.05.11}
}

@MISC{pdb,
  title = {RCSB Protein Data Bank},
  howpublished = {\url{http://www.pdb.org} (1.\,6.\,2010)}
}

@MISC{pdb-stats,
  title = {Protein Data Bank Statistics},
  howpublished = {\url{http://www.rcsb.org/pdb/static.do?p=general_information/pdb_statistics/index.html}
	(1.\,6.\,2010)},
  owner = {krab},
  timestamp = {2010.06.01}
}

@MISC{pdb-webdocs,
  title = {worldwide Protein Data Bank, File Format Documentation},
  howpublished = {\url{http://www.wwpdb.org/docs.html} (1.\,6.\,2010)},
  owner = {krab},
  timestamp = {2010.06.02}
}

@MISC{sql-faq-5,
  title = {SQLite Frequently Asked Questions, Can multiple applications or multiple
	instances of the same application access a single database file at
	the same time?},
  howpublished = {\url{http://www.sqlite.org/faq.html\#q5} (1.\,6.\,2010)}
}

@MISC{sql-whentouse,
  title = {Appropriate Uses For SQLite},
  howpublished = {\url{http://www.sqlite.org/whentouse.html} (1.\,6.\,2010)}
}

